Rosetta:MSF: a modular framework for multi-state computational protein design

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

(2016) Guanghong Wei et al.   CHEMICAL REVIEWS

Computational protein design for given backbone: recent progresses in general method-related aspects

(2016) Haiyan Liu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability

(2016) Adi Goldenzweig et al.   MOLECULAR CELL

De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity

(2016) S. E. Boyken et al.   SCIENCE

Computationally Designed Bispecific Antibodies using Negative State Repertoires

(2016) Andrew Leaver-Fay et al.   STRUCTURE

Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences

(2015) Alexander M. Sevy et al.   PLoS Computational Biology

Characterization of Two Distinct Modes of Drug Binding to Human Intestinal Fatty Acid Binding Protein

(2014) Rahul Patil et al.   ACS Chemical Biology

A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells

(2014) Erik Procko et al.   CELL

Exploration of Alternate Catalytic Mechanisms and Optimization Strategies for Retroaldolase Design

(2013) Sinisa Bjelic et al.   JOURNAL OF MOLECULAR BIOLOGY

Automating human intuition for protein design

(2013) Lucas G. Nivón et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles

(2013) James A. Davey et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

(2012) O. Khersonsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multistate approaches in computational protein design

(2012) James A. Davey et al.   PROTEIN SCIENCE

Robust design and optimization of retroaldol enzymes

(2012) Eric A. Althoff et al.   PROTEIN SCIENCE

A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds

(2012) P. Benjamin Stranges et al.   PROTEIN SCIENCE

Durandal: Fast exact clustering of protein decoys

(2011) Francois Berenger et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Anchored Design of Protein-Protein Interfaces

(2011) Steven M. Lewis et al.   PLoS One

De Novo Enzyme Design Using Rosetta3

(2011) Florian Richter et al.   PLoS One

A Generic Program for Multistate Protein Design

(2011) Andrew Leaver-Fay et al.   PLoS One

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

RosettaBackrub--a web server for flexible backbone protein structure modeling and design

(2010) F. Lauck et al.   NUCLEIC ACIDS RESEARCH

Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles

(2010) B. D. Allen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting resistance mutations using protein design algorithms

(2010) K. M. Frey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Design of protein-interaction specificity gives selective bZIP-binding peptides

(2009) Gevorg Grigoryan et al.   NATURE

Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes

(2009) Carola Engler et al.   PLoS One

X-ray vs. NMR structures as templates for computational protein design

(2009) Michael Schneider et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational design of second-site suppressor mutations at protein-protein interfaces

(2009) Deanne W. Sammond et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Design of Protein–Ligand Binding Based on the Molecular-Mechanics Energy Model

(2008) F. Edward Boas et al.   JOURNAL OF MOLECULAR BIOLOGY

A Simple Model of Backbone Flexibility Improves Modeling of Side-chain Conformational Variability

(2008) Gregory D. Friedland et al.   JOURNAL OF MOLECULAR BIOLOGY

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

RosettaLigand Docking with Full Ligand and Receptor Flexibility

(2008) Ian W. Davis et al.   JOURNAL OF MOLECULAR BIOLOGY

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE